wrangle
Author: Kaitlin Volk; with edits by Jeff Cegan
Date: May 19, 2021
Project HAB with Jodi Ryder
Load and filter data.
Summary of data:
## loc_id reservoir sample_num
## NRR20001: 60587 Length:1070160 200908190900000.0: 57
## GRR20001: 58858 Class :character 201508171200000.0: 56
## TAR20001: 57385 Mode :character 199208181200000.0: 52
## EFR20001: 53021 201409231200000.0: 51
## CRR20001: 47639 199206161200000.0: 48
## CCK20001: 45230 199207281200000.0: 48
## (Other) :747440 (Other) :1069848
## sample_date yr mo depth
## Min. :1965-04-18 Length:1070160 Length:1070160 Min. : 0.00
## 1st Qu.:1988-09-13 Class :character Class :character 1st Qu.: 10.00
## Median :1997-07-29 Mode :character Mode :character Median : 22.00
## Mean :1996-12-28 Mean : 26.73
## 3rd Qu.:2007-07-31 3rd Qu.: 40.00
## Max. :2019-12-12 Max. :999.00
##
## param value units
## temp_c :461627 Min. : -99.00 deg C :450676
## DO_mgl :419019 1st Qu.: 3.95 mg/l :421756
## DO_perc: 67556 Median : 11.00 mg/L : 82011
## TDS : 29568 Mean : 20.31 % : 63754
## P_total: 16284 3rd Qu.: 21.10 ug/l : 18289
## C_total: 16237 Max. :40300.00 Deg C : 10950
## (Other): 59869 (Other): 22724Exploring ChlA data with Plots
ChlA is an important variable for identifying HABs and for the correlations in 1.6 of the SOW
Two methods have been used: trichromatic and Spectrophotomatic. Is one better? Should they both be used?
###Look for outliers/weirdness in the variables
## Warning: Removed 11930 rows containing non-finite values (stat_qq).
## Warning: Removed 54539 rows containing non-finite values (stat_qq).
## Warning: Removed 472111 rows containing non-finite values (stat_qq).
## Warning: Removed 406000 rows containing non-finite values (stat_qq).
## Warning: Removed 461332 rows containing non-finite values (stat_qq).
## Warning: Removed 457343 rows containing non-finite values (stat_qq).
## Warning: Removed 457302 rows containing non-finite values (stat_qq).
###Dive into total phosphorous (P_total) 
###Clean the data
###Visualize the cleaned data
## Warning: Removed 11900 rows containing non-finite values (stat_qq).
## Warning: Removed 85802 rows containing non-finite values (stat_qq).
## Warning: Removed 471962 rows containing non-finite values (stat_qq).
## Warning: Removed 405852 rows containing non-finite values (stat_qq).
## Warning: Removed 461200 rows containing non-finite values (stat_qq).
## Warning: Removed 457211 rows containing non-finite values (stat_qq).
## Warning: Removed 457441 rows containing non-finite values (stat_qq).
##Curious about how many reserviors and sites per reservoir there are:
## # A tibble: 51 x 2
## reservoir n.sites
## <chr> <int>
## 1 BBL 5
## 2 BGR 1
## 3 BHR 30
## 4 BL1 1
## 5 BNV 4
## 6 BPR 3
## 7 BRR 78
## 8 BVR 28
## 9 BWR 2
## 10 CBR 15
## # … with 41 more rows1.2 Time series plots for a single location
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 18102## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 4.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at 18106## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.0004## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 0.0004## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## `geom_smooth()` using formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at 18102## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.0004## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 18102## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 16.16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## `summarise()` has grouped output by 'loc_id'. You can override using the `.groups` argument.## Warning in `[<-.factor`(`*tmp*`, list, value = 0): invalid factor level, NA
## generated## `summarise()` has grouped output by 'reservoir'. You can override using the `.groups` argument.## Warning: All formats failed to parse. No formats found.## `geom_smooth()` using formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at 18102## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.0004## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 18102## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 16.16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)## Warning: Removed 385 rows containing missing values (geom_text).
## `mutate_all()` ignored the following grouping variables:
## Column `reservoir`
## Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.1.3 Characterizing reservoirs based on last five years of summer months (may-sept)
Oligo Meso Eutro TP (ug/L) 8 27 84
TN (mg/L) .66 .75 1.9
ChlA (ug/L) 1.7 4.7 14
1.4 Assign reservoirs to mixing regime====
```{r. echo=FALSE}
## 1.5 Apply Mann-Kendall test to time series to find increasingtrends====
```{r. echo=FALSE}
1.6 Cross correlation of time series (esp. chla, our bloom indicator )
```{r. echo=FALSE}
```